Decoding ancient genomes: Genomics approaches and innovative species recognition pipeline for diadromous fish

International audience Understanding the evolution of wild species is crucial for developing effective population management strategies and predicting their future trajectories. In my doctoral research, we opted for genomics approaches to explore the demographic history of two iconic diadromous fish...

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Main Authors: Jacques, Patrick, Maman, Sarah, Béarez, Philippe, Nikolic, Natacha, Debruyne, Régis, Ephrem, Brice, Manicki, Aurélie, Klopp, Christophe, Sternberg, Myriam, Rognon, Gaston, Ransan, Léonard, Bellanger, Chloé, Chat, Joelle, Michel, Barbaza, Benoît, Clavel, Morgane, Dachary, Daujeard, Camille, Gey, Delphine, Émilie, Guillaud, Sheila, Hamilton-Dyer, Jennifer, Harland, Stéphan, Hinguant, Marie-Pierre, Horad-Herbin, Esmee, Hummel, Jagt, Van, Der, Leif, Jonsson, Stéphane, Madelaine, Daniel, Makowiecki, Liz, Quinlan, Schmölcke, Ulrich
Other Authors: Ecologie Comportementale et Biologie des Populations de Poissons (ECOBIOP), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Archéologie, Archéosciences, Histoire (CReAAH), Le Mans Université (UM)-Université de Rennes (UR)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC)-Nantes Université - UFR Histoire, Histoire de l'Art et Archéologie (Nantes Univ - UFR HHAA), Nantes Université - pôle Humanités, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Humanités, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Centre Camille Jullian - Histoire et archéologie de la Méditerranée et de l'Afrique du Nord de la protohistoire à la fin de l'Antiquité (CCJ), Aix Marseille Université (AMU)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Acquisition et Analyse de Données pour l'Histoire naturelle (2AD), Bournemouth University Poole (BU), University of the Highlands and Islands (UHI), Institut National de Recherche et d'Analyse Physico-Chimique (INRAP), Cités, Territoires, Environnement et Sociétés (CITERES), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), PBL Netherlands Environmental Assessment Agency, Cultural Heritage Agency of the Netherlands, Göteborgs Universitet = University of Gothenburg (GU), musée national de la préhistoire des Eyzies, Institute of Archaeology Poland, University of York York, UK, Bavarian State Collection of Zoology
Format: Conference Object
Language:English
Published: HAL CCSD 2024
Subjects:
Online Access:https://hal.inrae.fr/hal-04527107
https://hal.inrae.fr/hal-04527107v2/document
https://hal.inrae.fr/hal-04527107v2/file/poster_i3s_PJ_final_Online_V3.pdf
https://doi.org/10.13140/RG.2.2.12906.53442
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Summary:International audience Understanding the evolution of wild species is crucial for developing effective population management strategies and predicting their future trajectories. In my doctoral research, we opted for genomics approaches to explore the demographic history of two iconic diadromous fishes: Anguilla anguilla (European eel) and Salmo salar (Atlantic salmon). We aim to elucidate their adaptive responses to environmental changes. Setting this project apart is the sequencing and genotyping of both archaeological (aDNA) and modern DNAs samples. Our study encompasses archaeological samples from various locations across Europe, spanning a temporal range of 17,000 years-from the Paleolithic to the modern era. To accurately assign species to each sample, we developed DeFiS (Detect Fish Species), a pipeline relying on reference genomes and samples to analyze k-mers: fixed-size nucleotide sub-strings. The list of k-mers and their occurrences from specific dictionaries for both reference genomes and samples. By comparing the dictionaries of the samples with those of the references, we could assign each sample to a specific species. We are currently validating the pipeline using freely available modern samples of all European diadromous fish species found in public databases (NCBI, Essembl, and scientific paper). The aim is to provide a valuable resource for biological scientists. Our method offers a significant advancement in the species identification process for aDNA research. By accelerating and refining this crucial step we aim to contribute to future aDNA-based investigations by facilitating the work of biologists studying wild species evolutions.